Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate

Bioconversion of citrus waste into mucic acid by xylose-fermenting Saccharomyces cerevisiae

Mucic acid holds promise as a platform chemical for bio-based nylon synthesis; however, its biological production encounters challenges including low yield and productivity. In this study, an efficient and high-yield method for mucic acid production was developed by employing genetically engineered Saccharomyces cerevisiae expressing the NAD+-dependent uronate dehydrogenase (udh) gene. To overcome the NAD+ dependency for the conversion of pectin to mucic acid, xylose was utilized as a co-substrate. Through optimization of the udh expression system, the engineered strain achieved a notable output, producing 20 g/L mucic acid with a highest reported productivity of 0.83 g/L-h and a theoretical yield of 0.18 g/g when processing pectin-containing citrus peel waste. These results suggest promising industrial applications for the biological production of mucic acid. Additionally, there is potential to establish a viable bioprocess by harnessing pectin-rich fruit waste alongside xylose-rich cellulosic biomass as raw materials.

Production of 2,5-Furandicarboxylic Acid Methyl Esters from Pectin-Based Aldaric Acid: from Laboratory to Bench Scale

2,5-Furandicarboxylic acid (FDCA) is one of the most attractive emerging renewable monomers, which has gained interest especially in polyester applications, such as the production of polyethylene furanoate (PEF). Recently, the attention has shifted towards FDCA esters due to their better solubility as well as the easier purification and polymerisation compared to FDCA. In our previous work, we reported the synthesis of FDCA butyl esters by dehydration of aldaric acids as stable intermediates. Here, we present the synthesis of FDCA methyl esters in high yields from pectin-based galactaric acid using a solid acid catalyst. The process enables high substrate concentrations (up to 20 wt %) giving up to 50 mol % FDCA methyl esters with total furancarboxylates yields of up to 90 mol %. The synthesis was successfully scaled up from gram-scale to kilogram-scale in batch reactors showing the feasibility of the process. The stability of the catalyst was tested in re-use experiments. Purification of the crude product by vacuum distillation and precipitation gave furan-2,5-dimethylcarboxylate with a 98 % purity.

Use of ambr®250 to assess mucic acid production in fed-batch cultures of a marine Trichoderma sp. D-221704

Mucic acid, a diacid with potential use in the food, cosmetic, chemical and pharmaceutical industries, can be produced by microbial conversion of D-galacturonic acid, which is abundant in pectin. Using the ambr®250 bioreactor system, we found that a recently generated transformant (D-221704, formerly referred to as T2) of a marine Trichoderma species produced up to 53 g L-1 mucic acid in glucose-limited fed-batch culture with D-galacturonic acid in the feed at pH 4, with a yield of 0.99 g mucic acid per g D-galacturonic acid consumed. Yeast extract was not essential for high production, but increased the initial production rate. Reducing the amount of glucose as the co-substrate reduced the amount of mucic acid produced to 31 g L-1. Mucic acid could also be produced at pH values less than 4.0 (3.5 and 3.0), but the amount produced was less than at pH 4.0. Furthermore, the yield of mucic acid on D-galacturonic acid at the end of the cultivations (0.5 to 0.7 g g-1) at these low pH levels suggested that recovery may be more difficult at lower pH on account of the high level of crystal formation. Another strain engineered to produce mucic acid, Trichoderma reesei D-161646, produced only 31 g L-1 mucic acid under the conditions used with D-221704.

Chromohalobacter salixigens Uronate Dehydrogenase: Directed Evolution for Improved Thermal Stability and Mutant CsUDH-inc X-ray Crystal Structure

Chromohalobacter salixigens contains a uronate dehydrogenase termed CsUDH that can convert uronic acids to their corresponding C1,C6-dicarboxy aldaric acids, an important enzyme reaction applicable for biotechnological use of sugar acids. To increase the thermal stability of this enzyme for biotechnological processes, directed evolution using gene family shuffling was applied, and the hits selected from 2-tier screening of a shuffled gene family library contained in total 16 mutations, only some of which when examined individually appreciably increased thermal stability. Most mutations, while having minimal or no effect on thermal stability when tested in isolation, were found to exhibit synergy when combined; CsUDH-inc containing all 16 mutations had ΔK _t ^0.5 +18 °C, such that k _cat was unaffected by incubation for 1 hr at ~70 °C. X-ray crystal structure of CsUDH-inc showed tight packing of the mutated residue side-chains, and comparison of rescaled B-values showed no obvious differences between wild type and mutant structures. Activity of CsUDH-inc was severely depressed on glucuronic and galacturonic acids. Combining select combinations of only three mutations resulted in good or comparable activity on these uronic acids, while maintaining some improved thermostability with ΔK _t ^0.5 ~+ 10 °C, indicating potential to further thermally optimize CsUDH for hyperthermophilic reaction environments.

Increasing Lovastatin Production by Re-routing the Precursors Flow of Aspergillus terreus via Metabolic Engineering

Lovastatin is an anti-cholesterol medicine that is commonly prescribed to manage cholesterol levels, and minimise the risk of suffering from heart-related diseases. Aspergillus terreus (ATCC 20542) supplied with carbohydrates or sugar alcohols can produce lovastatin. The present work explored the application of metabolic engineering in A. terreus to re-route the precursor flow towards the lovastatin biosynthetic pathway by simultaneously overexpressing the gene for acetyl-CoA carboxylase (acc) to increase the precursor flux, and eliminate ( +)-geodin biosynthesis (a competing secondary metabolite) by removing the gene for emodin anthrone polyketide synthase (gedC). Alterations to metabolic flux in the double mutant (gedCΔ*acc^ox) strain and the effects of using two different substrate formulations were examined. The gedCΔ*acc^ox strain, when cultivated with a mixture of glycerol and lactose, significantly (p < 0.05) increased the levels of metabolic precursors malonyl-CoA (48%) and acetyl-CoA (420%), completely inhibited the (+)-geodin biosynthesis, and increased the level of lovastatin [152 mg/L; 143% higher than the wild-type (WT) strain]. The present work demonstrated how the manipulation of A. terreus metabolic pathways could increase the efficiency of carbon flux towards lovastatin, thus elevating its overall production and enabling the use of glycerol as a substrate source. As such, the present work also provides a framework model for other medically or industrially important fungi to synthesise valuable compounds using sustainable carbon sources.

Recent advances in the biological valorization of citrus peel waste into fuels and chemicals

In the quest to reduce global food loss and waste, fruit processing wastes, particularly citrus peel waste (CPW), have emerged as a promising and sustainable option for biorefinery without competing with human foods and animal feeds. CPW is largely produced and, as recent studies suggest, has the industrial potential of biological valorization into fuels and chemicals. In this review, the promising aspects of CPW as an alternative biomass were highlighted, focusing on its low lignin content. In addition, specific technical difficulties in fermenting CPW are described, highlighting that citrus peel is high in pectin that consist of non-fermentable sugars, mainly galacturonic acid. Last, recent advances in the metabolic engineering of yeast and other microbial strains that ferment CPW-derived sugars to produce value-added products, such as ethanol and mucic acid, are summarized. For industrially viable CPW-based biorefinery, more studies are needed to improve fermentation efficiency and to diversify product profiles.

Engineering marine fungi for conversion of D-galacturonic acid to mucic acid

BACKGROUND

Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid production, assessing the suitability of marine fungi for production of platform chemicals. The pathway for biotechnologcial production of mucic (galactaric) acid from D-galacturonic acid is simple and requires minimal modification of the genome, optimally one deletion and one insertion. D-Galacturonic acid, the main component of pectin, is a potential substrate for bioconversion, since pectin-rich waste is abundant.

RESULTS

Trichoderma sp. LF328 and Coniochaeta sp. MF729 were engineered using CRISPR-Cas9 to oxidize D-galacturonic acid to mucic acid, disrupting the endogenous pathway for D-galacturonic acid catabolism when inserting a gene encoding bacterial uronate dehydrogenase. The uronate dehydrogenase was expressed under control of a synthetic expression system, which fucntioned in both marine strains. The marine Trichoderma transformants produced 25 g L-1 mucic acid from D-galacturonic acid in equimolar amounts: the yield was 1.0 to 1.1 g mucic acid [g D-galacturonic acid utilized]-1. D-Xylose and lactose were the preferred co-substrates. The engineered marine Trichoderma sp. was more productive than the best Trichoderma reesei strain (D-161646) described in the literature to date, that had been engineered to produce mucic acid. With marine Coniochaeta transformants, D-glucose was the preferred co-substrate, but the highest yield was 0.82 g g-1: a portion of D-galacturonic acid was still metabolized. Coniochaeta sp. transformants produced adequate pectinases to produce mucic acid from pectin, but Trichoderma sp. transformants did not.

CONCLUSIONS

Both marine species were successfully engineered using CRISPR-Cas9 and the synthetic expression system was functional in both species. Although Coniochaeta sp. transformants produced mucic acid directly from pectin, the metabolism of D-galacturonic acid was not completely disrupted and mucic acid amounts were low. The D-galacturonic pathway was completely disrupted in the transformants of the marine Trichoderma sp., which produced more mucic acid than a previously constructed T. reesei mucic acid producing strain, when grown under similar conditions. This demonstrated that marine fungi may be useful as production organisms, not only for native enzymes or bioactive compounds, but also for other compounds.

Furan-2,5- and Furan-2,3-dicarboxylate Esters Derived from Marine Biomass as Plasticizers for Poly(vinyl chloride)

Esters of furan dicarboxylic acids (DAFs) were synthesized by a one-pot reaction between marine biomass-derived galactaric acid and bioalcohol under solvent-free conditions and were fully characterized. The catalyst amount could be reduced without loss of reaction yields using p-xylene as the material separation agent. Also, a possible mechanism was proposed for the first time. Then the properties of four DAFs as plasticizers on the poly(vinyl chloride) (PVC) matrix were investigated. The experimental results showed that DAFs exhibit competitive efficiencies of plasticization when compared to the most commercialized plasticizer, DOP. It was found that the combination of DAFs and PVC produced homogeneous smooth-surface films, indicating miscibility between them. ATR-FTIR depicted the upshift of carbonyl absorption bands after mixing with the PVC matrix, with a magnitude of at most 18-21 cm-1. TGA, DSC, and UTM data illustrated equivalent plasticization efficiencies. Due to their small molecular weights, the investigated DAFs are more volatile. However, due to bearing an oxygen atom in the aromatic furan ring, the degree of polarization of DAFs was boosted and helped inhibit leaching into the surrounding media. In brief, these synthetic compounds have promising feasibility as biobased plasticizers. Moreover, another interesting point is that the properties of furan-2,3-dicarboxylic acid derivatives were studied for the first time and herein reported.

Production of Hexaric Acids from Biomass

Sugar acids obtained by aldohexose oxidation of both the terminal aldehyde group and the hydroxy group at the other end to carboxyl groups are called hexaric acids (i.e., six-carbon aldaric acids). Because hexaric acids have four secondary hydroxy groups that are stereochemically diverse and two carboxyl groups, various applications of these acids have been studied. Conventionally, hexaric acids have been produced mainly by nitric acid oxidation of aldohexose, but full-scale commercialization has not been realized; there are many problems regarding yield, safety, environmental burden, etc. In recent years, therefore, improvements in hexaric acid production by nitric acid oxidation have been made, while new production methods, including biocatalytic methods, are actively being studied. In this paper, we summarize these production methods in addition to research on the application of hexaric acids.

Development of microtiter plate scale CRISPR/Cas9 transformation method for Aspergillus niger based on in vitro assembled ribonucleoprotein complexes

Background

The CRISPR/Cas9 is currently the predominant technology to enhance the genome editing efficiency in eukaryotes. Established tools for many fungal species exist while most of them are based on in vivo expressed Cas9 and guide RNA (gRNA). Alternatively, in vitro assembled Cas9 and gRNA ribonucleoprotein complexes can be used in genome editing, however, only a few examples have been reported in fungi. In general, high-throughput compatible transformation workflows for filamentous fungi are immature.

Results

In this study, a CRISPR/Cas9 facilitated transformation and genome editing method based on in vitro assembled ribonucleoprotein complexes was developed for the filamentous fungus Aspergillus niger. The method was downscaled to be compatible with 96-well microtiter plates. The optimized method resulted in 100% targeting efficiency for a single genomic target. After the optimization, the method was demonstrated to be suitable for multiplexed genome editing with two or three genomic targets in a metabolic engineering application. As a result, an A. niger strain with improved capacity to produce galactarate, a potential chemical building block, was generated.

Conclusions

The developed microtiter plate compatible CRISPR/Cas9 method provides a basis for high-throughput genome editing workflows in A. niger and other related species. In addition, it improves the cost-effectiveness of CRISPR/Cas9 genome editing methods in fungi based on in vitro assembled ribonucleoproteins. The demonstrated metabolic engineering example with multiplexed genome editing highlights the applicability of the method.

Electronic supplementary material

The online version of this article (10.1186/s40694-019-0066-9) contains supplementary material, which is available to authorized users.

Microbial hexuronate catabolism in biotechnology

The most abundant hexuronate in plant biomass is D-galacturonate. D-Galacturonate is the main constituent of pectin. Pectin-rich biomass is abundantly available as sugar beet pulp or citrus processing waste and is currently mainly used as cattle feed. Other naturally occurring hexuronates are D-glucuronate, L-guluronate, D-mannuronate and L-iduronate. D-Glucuronate is a constituent of the plant cell wall polysaccharide glucuronoxylan and of the algal polysaccharide ulvan. Ulvan also contains L-iduronate. L-Guluronate and D-mannuronate are the monomers of alginate. These raw materials have the potential to be used as raw material in biotechnology-based production of fuels or chemicals. In this communication, we will review the microbial pathways related to these hexuronates and their potential use in biotechnology.

Spotlight on fungal pectin utilization-from phytopathogenicity to molecular recognition and industrial applications

Pectin is a complex polysaccharide with D-galacturonic acid as its main component that predominantly accumulates in the middle lamella of the plant cell wall. Integrity and depolymerization of pectic structures have long been identified as relevant factors in fungal phytosymbiosis and phytopathogenicity in the context of tissue penetration and carbon source supply. While the pectic content of a plant cell wall can vary significantly, pectin was reported to account for up to 20-25% of the total dry weight in soft and non-woody tissues with non- or mildly lignified secondary cell walls, such as found in citrus peel, sugar beet pulp, and apple pomace. Due to their potential applications in various industrial sectors, pectic sugars from these and similar agricultural waste streams have been recognized as valuable targets for a diverse set of biotechnological fermentations.Recent advances in uncovering the molecular regulation mechanisms for pectinase expression in saprophytic fungi have led to a better understanding of fungal pectin sensing and utilization that could help to improve industrial, pectin-based fermentations. Related research in phytopathogenic fungi has furthermore added to our knowledge regarding the relevance of pectinases in plant cell wall penetration during onset of disease and is therefore highly relevant for agricultural sciences and the agricultural industry. This review therefore aims at summarizing (i) the role of pectinases in phytopathogenicity, (ii) the global regulation patterns for pectinase expression in saprophytic filamentous fungi as a highly specialized class of pectin degraders, and (iii) the current industrial applications in pectic sugar fermentations and transformations.

Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste

Pectin-rich biomasses, such as citrus peel and sugar beet pulp, hold promise as inexpensive feedstocks for microbial fermentations as enzymatic hydrolysis of their component polysaccharides can be accomplished inexpensively to yield high concentrations of fermentable sugars and D-galacturonic acid (D-galUA). In this study, we tackle a number of challenges associated with engineering a microbial strain to convert pectin-rich hydrolysates into commodity and specialty chemicals. First, we engineer D-galUA utilization into yeast, Saccharomyces cerevisiae. Second, we identify that the mechanism of D-galUA uptake into yeast is mediated by hexose transporters and that consumption of D-galUA is inhibited by D-glucose. Third, we enable co-utilization of D-galUA and D-glucose by identifying and expressing a heterologous transporter, GatA, from Aspergillus niger. Last, we demonstrate the use of this transporter for production of the platform chemical, meso-galactaric acid, directly from industrial Navel orange peel waste.

A community-driven reconstruction of the Aspergillus niger metabolic network

Background

Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected and integrated in a genome-scale model to devise strategies for improving its performance as a host organism.

Results

In this paper, we update an existing model of A. niger metabolism to include the information collected from 876 publications, thereby expanding the coverage of the model by 940 reactions, 777 metabolites and 454 genes. In the presented consensus genome-scale model of A. niger iJB1325 , we integrated experimental data from publications and patents, as well as our own experiments, into a consistent network. This information has been included in a standardized way, allowing for automated testing and continuous improvements in the future. This repository of experimental data allowed the definition of 471 individual test cases, of which the model complies with 373 of them. We further re-analyzed existing transcriptomics and quantitative physiology data to gain new insights on metabolism. Additionally, the model contains 3482 checks on the model structure, thereby representing the best validated genome-scale model on A. niger developed until now. Strain-specific model versions for strains ATCC 1015 and CBS 513.88 have been created containing all data used for model building, thereby allowing users to adopt the models and check the updated version against the experimental data. The resulting model is compliant with the SBML standard and therefore enables users to easily simulate it using their preferred software solution.

Conclusion

Experimental data on most organisms are scattered across hundreds of publications and several repositories.To allow for a systems level understanding of metabolism, the data must be integrated in a consistent knowledge network. The A. niger iJB1325 model presented here integrates the available data into a highly curated genome-scale model to facilitate the simulation of flux distributions, as well as the interpretation of other genome-scale data by providing the metabolic context.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0060-7) contains supplementary material, which is available to authorized users.

Overexpression of acetyl-CoA carboxylase in Aspergillus terreus to increase lovastatin production

The present work describes the application of homologous recombination techniques in a wild-type Aspergillus terreus (ATCC 20542) strain to increase the flow of precursors towards the lovastatin biosynthesis pathway. A new strain was generated to overexpress acetyl-CoA carboxylase (ACCase) by replacing the native ACCase promoter with a strong constitutive PadhA promoter from Aspergillus nidulans. Glycerol and a mixture of lactose and glycerol were used independently as the carbon feedstock to determine the degree of response by the A. terreus strains towards the production of acetyl-CoA, and malonyl-CoA. The new strain increased the levels of malonyl-CoA and acetyl-CoA by 240% and 14%, respectively, compared to the wild-type strain. As a result, lovastatin production was increased by 40% and (+)-geodin was decreased by 31% using the new strain. This study shows for the first time that the metabolism of Aspergillus terreus can be manipulated to attain higher levels of precursors and valuable secondary metabolites.

Scaling up and scaling down the production of galactaric acid from pectin using Trichoderma reesei

Background

Bioconversion of d-galacturonic acid to galactaric (mucic) acid has previously been carried out in small scale (50–1000 mL) cultures, which produce tens of grams of galactaric acid. To obtain larger amounts of biologically produced galactaric acid, the process needed to be scaled up using a readily available technical substrate. Food grade pectin was selected as a readily available source of d-galacturonic acid for conversion to galactaric acid.

Results

We demonstrated that the process using Trichoderma reesei QM6a Δgar1 udh can be scaled up from 1 L to 10 and 250 L, replacing pure d-galacturonic acid with commercially available pectin. T. reesei produced 18 g L⁻¹ galactaric acid from food-grade pectin (yield 1.00 g [g d-galacturonate consumed]⁻¹) when grown at 1 L scale, 21 g L⁻¹ galactaric acid (yield 1.11 g [g d-galacturonate consumed]⁻¹) when grown at 10 L scale and 14 g L⁻¹ galactaric acid (yield 0.77 g [g d-galacturonate consumed]⁻¹) when grown at 250 L scale. Initial production rates were similar to those observed in 500 mL cultures with pure d-galacturonate as substrate. Approximately 2.8 kg galactaric acid was precipitated from the 250 L culture, representing a recovery of 77% of the galactaric acid in the supernatant. In addition to scaling up, we also demonstrated that the process could be scaled down to 4 mL for screening of production strains in 24-well plate format. Production of galactaric acid from pectin was assessed for three strains expressing uronate dehydrogenase under alternative promoters and up to 11 g L⁻¹ galactaric acid were produced in the batch process.

Conclusions

The process of producing galactaric acid by bioconversion with T. reesei was demonstrated to be equally efficient using pectin as it was with d-galacturonic acid. The 24-well plate batch process will be useful screening new constructs, but cannot replace process optimisation in bioreactors. Scaling up to 250 L demonstrated good reproducibility with the smaller scale but there was a loss in yield at 250 L which indicated that total biomass extraction and more efficient DSP would both be needed for a large scale process.

The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger

In Aspergillus niger, the enzymes encoded by gaaA, gaaB, and gaaC catabolize d‐galacturonic acid (GA) consecutively into l‐galactonate, 2‐keto‐3‐deoxy‐l‐galactonate, pyruvate, and l‐glyceraldehyde, while GaaD converts l‐glyceraldehyde to glycerol. Deletion of gaaB or gaaC results in severely impaired growth on GA and accumulation of l‐galactonate and 2‐keto‐3‐deoxy‐l‐galactonate, respectively. Expression levels of GA‐responsive genes are specifically elevated in the ∆gaaC mutant on GA as compared to the reference strain and other GA catabolic pathway deletion mutants. This indicates that 2‐keto‐3‐deoxy‐l‐galactonate is the inducer of genes required for GA utilization.

Clustered Genes Encoding 2-Keto-l-Gulonate Reductase and l-Idonate 5-Dehydrogenase in the Novel Fungal d-Glucuronic Acid Pathway

D-Glucuronic acid is a biomass component that occurs in plant cell wall polysaccharides and is catabolized by saprotrophic microorganisms including fungi. A pathway for D-glucuronic acid catabolism in fungal microorganisms is only partly known. In the filamentous fungus Aspergillus niger, the enzymes that are known to be part of the pathway are the NADPH requiring D-glucuronic acid reductase forming L-gulonate and the NADH requiring 2-keto-L-gulonate reductase that forms L-idonate. With the aid of RNA sequencing we identified two more enzymes of the pathway. The first is a NADPH requiring 2-keto-L-gulonate reductase that forms L-idonate, GluD. The second is a NAD⁺ requiring L-idonate 5-dehydrogenase forming 5-keto-gluconate, GluE. The genes coding for these two enzymes are clustered and share the same bidirectional promoter. The GluD is an enzyme with a strict requirement for NADP⁺/NADPH as cofactors. The k_cat for 2-keto-L-gulonate and L-idonate is 21.4 and 1.1 s^-1, and the K_m 25.3 and 12.6 mM, respectively, when using the purified protein. In contrast, the GluE has a strict requirement for NAD⁺/NADH. The k_cat for L-idonate and 5-keto-D-gluconate is 5.5 and 7.2 s^-1, and the K_m 30.9 and 8.4 mM, respectively. These values also refer to the purified protein. The gluD deletion resulted in accumulation of 2-keto-L-gulonate in the liquid cultivation while the gluE deletion resulted in reduced growth and cessation of the D-glucuronic acid catabolism.

Engineering Aspergillus niger for galactaric acid production: elimination of galactaric acid catabolism by using RNA sequencing and CRISPR/Cas9

Background

meso-Galactaric acid is a dicarboxylic acid that can be produced by the oxidation of d-galacturonic acid, the main constituent of pectin. Mould strains can be engineered to perform this oxidation by expressing the bacterial enzyme uronate dehydrogenase. In addition, the endogenous pathway for d-galacturonic acid catabolism has to be inactivated. The filamentous fungus Aspergillus niger would be a suitable strain for galactaric acid production since it is efficient in pectin hydrolysis, however, it is catabolizing the resulting galactaric acid via an unknown catabolic pathway.

Results

In this study, a transcriptomics approach was used to identify genes involved in galactaric acid catabolism. Several genes were deleted using CRISPR/Cas9 together with in vitro synthesized sgRNA. As a result, galactaric acid catabolism was disrupted. An engineered A. niger strain combining the disrupted galactaric and d-galacturonic acid catabolism with an expression of a heterologous uronate dehydrogenase produced galactaric acid from d-galacturonic acid. The resulting strain was also converting pectin-rich biomass to galactaric acid in a consolidated bioprocess.

Conclusions

In the present study, we demonstrated the use of CRISPR/Cas9 mediated gene deletion technology in A. niger in an metabolic engineering application. As a result, a strain for the efficient production of galactaric acid from d-galacturonic acid was generated. The present study highlights the usefulness of CRISPR/Cas9 technology in the metabolic engineering of filamentous fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0613-5) contains supplementary material, which is available to authorized users.

The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin

We identified the d-galacturonic acid (GA)-responsive transcriptional activator GaaR of the saprotrophic fungus, Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell, and to induce the GA catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to the expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides other than GA.

A novel pathway for fungal D-glucuronate catabolism contains an L-idonate forming 2-keto-L-gulonate reductase

For the catabolism of D-glucuronate, different pathways are used by different life forms. The pathways in bacteria and animals are established, however, a fungal pathway has not been described. In this communication, we describe an enzyme that is essential for D-glucuronate catabolism in the filamentous fungus Aspergillus niger. The enzyme has an NADH dependent 2-keto-L-gulonate reductase activity forming L-idonate. The deletion of the corresponding gene, the gluC, results in a phenotype of no growth on D-glucuronate. The open reading frame of the A. niger 2-keto-L-gulonate reductase was expressed as an active protein in the yeast Saccharomyces cerevisiae. A histidine tagged protein was purified and it was demonstrated that the enzyme converts 2-keto-L-gulonate to L-idonate and, in the reverse direction, L-idonate to 2-keto-L-gulonate using the NAD(H) as cofactors. Such an L-idonate forming 2-keto-L-gulonate dehydrogenase has not been described previously. In addition, the finding indicates that the catabolic D-glucuronate pathway in A. niger differs fundamentally from the other known D-glucuronate pathways.

A novel Zn2 Cys6 transcription factor BcGaaR regulates D-galacturonic acid utilization in Botrytis cinerea

D-galacturonic acid (GalA) is the most abundant monosaccharide component of pectin. Previous transcriptome analysis in the plant pathogenic fungus Botrytis cinerea identified eight GalA-inducible genes involved in pectin decomposition, GalA transport and utilization. Co-expression of these genes indicates that a specific regulatory mechanism occurs in B. cinerea. In this study, promoter regions of these genes were analysed and eight conserved sequence motifs identified. The Bclga1 promoter, containing all these motifs, was functionally analysed and the motif designated GalA Responsive Element (GARE) was identified as the crucial cis-regulatory element in regulation of GalA utilization in B. cinerea. Yeast one-hybrid screening with the GARE motif led to identification of a novel Zn2 Cys6 transcription factor (TF), designated BcGaaR. Targeted knockout analysis revealed that BcGaaR is required for induction of GalA-inducible genes and growth of B. cinerea on GalA. A BcGaaR-GFP fusion protein was predominantly localized in nuclei in mycelium grown in GalA. Fluorescence in nuclei was much stronger in mycelium grown in GalA, as compared to fructose and glucose. This study provides the first report of a GalA-specific TF in filamentous fungi. Orthologs of BcGaaR are present in other ascomycete fungi that are able to utilize GalA, including Aspergillus spp., Trichoderma reesei and Neurospora crassa.

Engineering a filamentous fungus for L-rhamnose extraction

L-Rhamnose is a high value rare sugar that is used as such or after chemical conversions. It is enriched in several biomass fractions such as the pectic polysaccharides rhamnogalacturonan I and II and in naringin, hesperidin, rutin, quercitrin and ulvan. We engineered the filamentous fungus Aspergillus niger to not consume L-rhamnose, while it is still able to produce the enzymes for the hydrolysis of L-rhamnose rich biomass. As a result we present a strain that can be used for the extraction of L-rhamnose in a consolidated process. In the process the biomass is hydrolysed to the monomeric sugars which are consumed by the fungus leaving the L-rhamnose.

Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.

Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway

Uronate dehydrogenases catalyse the oxidation of uronic acids to aldaric acids, which represent ‘top value-added chemicals’ that have the potential to substitute petroleum-derived chemicals. The identification and annotation of three uronate dehydrogenases derived from Fulvimarina pelagi HTCC2506, Streptomyces viridochromogenes DSM 40736 and Oceanicola granulosus DSM 15982 via sequence analysis is described. Characterization and comparison with two known uronate dehydrogenases in regard to substrate spectrum, catalytic activity and pH as well as temperature dependence was performed. The catalytic efficiency was investigated in two different buffer systems; potassium phosphate and Tris-HCl. In addition to the typical and well available substrates glucuronate and galacturonate also mannuronate as part of many structural polysaccharides were tested. The uronate dehydrogenase of Agrobacterium tumefaciens and Pseudomonas syringae showed catalytic dependency on the buffer system resulting in an increased K_m especially for glucuronate in potassium phosphate compared with Tris-HCl buffer. Enzyme stability at 37°C of the different Udhs was in the order: P. syringae < S. viridochromogens < A. tumefaciens < F. pelagi < O. granulosus. All enzymes showed activity within a broad pH range from 7.0 to 9.5, only O. granulosus had a very narrow range around 7.0.

Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production

Background

Synthetic L-ascorbic acid (vitamin C) is widely used as a preservative and nutrient in food and pharmaceutical industries. In the current production method, D-glucose is converted to L-ascorbic acid via several biochemical and chemical steps. The main source of L-ascorbic acid in human nutrition is plants. Several alternative metabolic pathways for L-ascorbic acid biosynthesis are known in plants. In one of them, D-galacturonic acid is the precursor. D-Galacturonic acid is also the main monomer in pectin, a plant cell wall polysaccharide. Pectin is abundant in biomass and is readily available from several waste streams from fruit and sugar processing industries.

Results

In the present work, we engineered the filamentous fungus Aspergillus niger for the conversion of D-galacturonic acid to L-ascorbic acid. In the generated pathway, the native D-galacturonate reductase activity was utilized while the gene coding for the second enzyme in the fungal D-galacturonic acid pathway, an L-galactonate consuming dehydratase, was deleted. Two heterologous genes coding for enzymes from the plant L-ascorbic acid pathway – L-galactono-1,4-lactone lactonase from Euglena gracilis (EgALase) and L-galactono-1,4-lactone dehydrogenase from Malpighia glabra (MgGALDH) – were introduced into the A. niger strain. Alternatively, an unspecific L-gulono-1,4-lactone lactonase (smp30) from the animal L-ascorbic acid pathway was introduced in the fungal strain instead of the plant L-galactono-1,4-lactone lactonase. In addition, a strain with the production pathway inducible with D-galacturonic acid was generated by using a bidirectional and D-galacturonic acid inducible promoter from the fungus. Even though, the lactonase enzyme activity was not observed in the resulting strains, they were capable of producing L-ascorbic acid from pure D-galacturonic acid or pectin-rich biomass in a consolidated bioprocess. Product titers up to 170 mg/l were achieved.

Conclusions

In the current study, an L-ascorbic acid pathway using D-galacturonic acid as a precursor was introduced to a microorganism for the first time. This is also the first report on an engineered filamentous fungus for L-ascorbic acid production and a proof-of-concept of consolidated bioprocess for the production.

Selective oxidation of uronic acids into aldaric acids over gold catalyst

Uronic acids available from hemicelluloses were oxidized into aldaric acids, valuable building block chemicals. Au/Al₂O₃ oxidized glucuronic and galacturonic acids quantitatively to the corresponding glucaric and galactaric acids at mild conditions.

Biochemical characterization of uronate dehydrogenases from three Pseudomonads, Chromohalobacter salixigens, and Polaromonas naphthalenivorans

Enzyme catalysts will be vital in the development of synthetic biology approaches for converting pectinic monosaccharides from citrus and beet processing waste streams to value-added materials. We describe here the biophysical and mechanistic characterization of uronate dehydrogenases from a wide variety of bacterial sources that convert galacturonic acid, the predominate building block of pectin from these plant sources, and glucuronic acid to their corresponding dicarboxylic acids galactarate and glucarate, the latter being a DOE top value biochemical from biomass. The enzymes from Pseudomonas syringae and Polaromonas naphthalenivorans were found to have the highest reported kcat(glucuronic acid) values, on the order of 220-270 s(-1). The thermal stability of this enzyme type is described for the first time here, where it was found that the Kt((0.5)) value range was >20 °C, and the enzyme from Chromohalobacter was moderately thermostable with Kt((0.5))=62.2 °C. The binding mechanism for these bi-substrate enzymes was also investigated in initial rate experiments, where a predominately steady-state ordered binding pattern was indicated.

Conversion of orange peel to L-galactonic acid in a consolidated process using engineered strains of Aspergillus niger

Citrus processing waste is a leftover from the citrus processing industry and is available in large amounts. Typically, this waste is dried to produce animal feed, but sometimes it is just dumped. Its main component is the peel, which consists mostly of pectin, with D-galacturonic acid as the main monomer. Aspergillus niger is a filamentous fungus that efficiently produces pectinases for the hydrolysis of pectin and uses the resulting D-galacturonic acid and most of the other components of citrus peel for growth. We used engineered A. niger strains that were not able to catabolise D-galacturonic acid, but instead converted it to L-galactonic acid. These strains also produced pectinases for the hydrolysis of pectin and were used for the conversion of pectin in orange peel to L-galactonic acid in a consolidated process. The D-galacturonic acid in the orange peel was converted to L-galactonic acid with a yield close to 90%. Submerged and solid-state fermentation processes were compared.

Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes

BACKGROUND

Pectin-rich agricultural wastes potentially represent favorable feedstocks for the sustainable production of alternative energy and bio-products. Their efficient utilization requires the conversion of all major constituent sugars. The current inability of the popular fermentation host Saccharomyces cerevisiae to metabolize the major pectic monosaccharide D-galacturonic acid (D-GalA) significantly hampers these efforts. While it has been reasoned that the optimization of cellular D-GalA uptake will be critical for the engineering of D-GalA utilization in yeast, no dedicated eukaryotic transport protein has been biochemically described. Here we report for the first time such a eukaryotic D-GalA transporter and characterize its functionality in S. cerevisiae.

RESULTS

We identified and characterized the D-GalA transporter GAT-1 out of a group of candidate genes obtained from co-expression analysis in N. crassa. The N. crassa Δgat-1 deletion strain is substantially affected in growth on pectic substrates, unable to take up D-GalA, and impaired in D-GalA-mediated signaling events. Moreover, expression of a gat-1 construct in yeast conferred the ability for strong high-affinity D-GalA accumulation rates, providing evidence for GAT-1 being a bona fide D-GalA transport protein. By recombinantly co-expressing D-galacturonate reductase or uronate dehydrogenase in yeast we furthermore demonstrated a transporter-dependent conversion of D-GalA towards more reduced (L-galactonate) or oxidized (meso-galactaric acid) downstream products, respectively, over a broad concentration range.

CONCLUSIONS

By utilizing the novel D-GalA transporter GAT-1 in S. cerevisiae we successfully generated a transporter-dependent uptake and catalysis system for D-GalA into two products with high potential for utilization as platform chemicals. Our data thereby provide a considerable first step towards a more complete utilization of biomass for biofuel and value-added chemicals production.

Categorisation of sugar acid dehydratases in Aspergillus niger

In the genome of Aspergillus niger five genes were identified coding for proteins with homologies to sugar acid dehydratases. The open reading frames were expressed in Saccharomyces cerevisiae and the activities tested with a library of sugar acids. Four genes were identified to code for proteins with activities with sugar acids: an l-galactonate dehydratase (gaaB), two d-galactonate dehydratases (dgdA, dgdB) and an l-rhamnonate dehydratase (lraC). The specificities of the proteins were characterised. The l-galactonate dehydratase had highest activity with l-fuconate, however it is unclear whether the enzyme is involved in l-fuconate catabolism. None of the proteins showed activity with galactaric acid or galactarolactone.

Low pH D-xylonate production with Pichia kudriavzevii

D-xylonic acid is one of the top 30 most desirable chemicals to be derived from biomass sugars identified by the US Department of Energy, being applicable as a non-food substitute for D-gluconic acid and as a platform chemical. We engineered the non-conventional yeast Pichia kudriavzevii VTT C-79090T to express a D-xylose dehydrogenase coding gene from Caulobacter crescentus. With this single modification the recombinant P. kudriavzevii strain produced up to 171 g L(-1) of D-xylonate from 171 g L(-1) D-xylose at a rate of 1.4 g L(-1) h(-1) and yield of 1.0 g [g substrate consumed](-1), which was comparable with D-xylonate production by Gluconobacter oxydans or Pseudomonas sp. The productivity of the strain was also remarkable at low pH, producing 146 g L(-1) D-xylonate at 1.2 g L(-1) h(-1) at pH 3.0. This is the best low pH production reported for D-xylonate. These results encourage further development towards industrial scale production.

Botrytis cinerea mutants deficient in D-galacturonic acid catabolism have a perturbed virulence on Nicotiana benthamiana and Arabidopsis, but not on tomato

D-Galacturonic acid is the most abundant monosaccharide component of pectic polysaccharides that comprise a significant part of most plant cell walls. Therefore, it is potentially an important nutritional factor for Botrytis cinerea when it grows in and through plant cell walls. The d-galacturonic acid catabolic pathway in B. cinerea consists of three catalytic steps converting d-galacturonic acid to pyruvate and l-glyceraldehyde, involving two nonhomologous galacturonate reductase genes (Bcgar1 and Bcgar2), a galactonate dehydratase gene (Bclgd1) and a 2-keto-3-deoxy-l-galactonate aldolase gene (Bclga1). Knockout mutants in each step of the pathway (ΔBcgar1/ΔBcgar2, ΔBclgd1 and ΔBclga1) showed reduced virulence on Nicotiana benthamiana and Arabidopsis thaliana leaves, but not on Solanum lycopersicum leaves. The cell walls of N. benthamiana and A. thaliana leaves were shown to have a higher d-galacturonic acid content relative to those of S. lycopersicum. The observation that mutants displayed a reduction in virulence, especially on plants with a high d-galacturonic acid content in the cell walls, suggests that, in these hosts, d-galacturonic acid has an important role as a carbon nutrient for B. cinerea. However, additional in vitro growth assays with the knockout mutants revealed that B. cinerea growth is reduced when d-galacturonic acid catabolic intermediates cannot proceed through the entire pathway, even when fructose is present as the major, alternative carbon source. These data suggest that the reduced virulence of d-galacturonic acid catabolism-deficient mutants on N. benthamiana and A. thaliana is not only a result of the inability of the mutants to utilize an abundant carbon source as nutrient, but also a result of the growth inhibition by catabolic intermediates.

Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid

D-Galacturonic acid, the main monomer of pectin, is an attractive substrate for bioconversions, since pectin-rich biomass is abundantly available and pectin is easily hydrolyzed. l-Galactonic acid is an intermediate in the eukaryotic pathway for d-galacturonic acid catabolism, but extracellular accumulation of l-galactonic acid has not been reported. By deleting the gene encoding l-galactonic acid dehydratase (lgd1 or gaaB) in two filamentous fungi, strains were obtained that converted d-galacturonic acid to l-galactonic acid. Both Trichoderma reesei Δlgd1 and Aspergillus niger ΔgaaB strains produced l-galactonate at yields of 0.6 to 0.9 g per g of substrate consumed. Although T. reesei Δlgd1 could produce l-galactonate at pH 5.5, a lower pH was necessary for A. niger ΔgaaB. Provision of a cosubstrate improved the production rate and titer in both strains. Intracellular accumulation of l-galactonate (40 to 70 mg g biomass(-1)) suggested that export may be limiting. Deletion of the l-galactonate dehydratase from A. niger was found to delay induction of d-galacturonate reductase and overexpression of the reductase improved initial production rates. Deletion of the l-galactonate dehydratase from A. niger also delayed or prevented induction of the putative d-galacturonate transporter An14g04280. In addition, A. niger ΔgaaB produced l-galactonate from polygalacturonate as efficiently as from the monomer.

The use of N,N'-diallylaldardiamides as cross-linkers in xylan derivatives-based hydrogels

N,N'-Diallylaldardiamides (DA) were synthesized from galactaric, xylaric, and arabinaric acids, and used as cross-linkers together with xylan (X) derivatives to create new bio-based hydrogels. Birch pulp extracted xylan was derivatized to different degrees of substitution of 1-allyloxy-2-hydroxy-propyl (A) groups combined with 1-butyloxy-2-hydroxy-propyl (B) and/or hydroxypropyl (HP) groups. The hydrogels were prepared in water solution by UV induced free-radical cross-linking polymerization of derivatized xylan polymers without DA cross-linker (xylan derivative hydrogel) or in the presence of 1 or 5 wt% of DA cross-linker (DA hydrogel). Commercially available cross-linker (+)-N,N'-diallyltartardiamide (DAT) was also used. The degree of substitution (DS) of A, B, and HP groups in xylan derivatives was analyzed according to (1)H NMR spectra. The DS values for the cross-linkable A groups of the derivatized xylans were 0.4 (HPX-A), 0.2 (HPX-BA), and 0.4 (X-BA). The hydrogels were examined with FT-IR and elemental analysis which proved the cross-linking successful. Water absorption of the hydrogels was examined in deionized water. Swelling degrees up to 350% were observed. The swollen morphology of the hydrogels was assessed by scanning electron microscopy (SEM). The presence of cross-linkers in DA hydrogels had only a small impact on the water absorbency when compared to xylan derivative hydrogels but a more uniform pore structure was achieved.

The D-galacturonic acid catabolic pathway in Botrytis cinerea

D-galacturonic acid is the most abundant component of pectin, one of the major polysaccharide constituents of plant cell walls. Galacturonic acid potentially is an important carbon source for microorganisms living on (decaying) plant material. A catabolic pathway was proposed in filamentous fungi, comprising three enzymatic steps, involving D-galacturonate reductase, L-galactonate dehydratase, and 2-keto-3-deoxy-L-galactonate aldolase. We describe the functional, biochemical and genetic characterization of the entire D-galacturonate-specific catabolic pathway in the plant pathogenic fungus Botrytis cinerea. The B. cinerea genome contains two non-homologous galacturonate reductase genes (Bcgar1 and Bcgar2), a galactonate dehydratase gene (Bclgd1), and a 2-keto-3-deoxy-L-galactonate aldolase gene (Bclga1). Their expression levels were highly induced in cultures containing GalA, pectate, or pectin as the sole carbon source. The four proteins were expressed in Escherichia coli and their enzymatic activity was characterized. Targeted gene replacement of all four genes in B. cinerea, either separately or in combinations, yielded mutants that were affected in growth on D-galacturonic acid, pectate, or pectin as the sole carbon source. In Aspergillus nidulans and A. niger, the first catabolic conversion only involves the Bcgar2 ortholog, while in Hypocrea jecorina, it only involves the Bcgar1 ortholog. In B. cinerea, however, BcGAR1 and BcGAR2 jointly contribute to the first step of the catabolic pathway, albeit to different extent. The virulence of all B. cinerea mutants in the D-galacturonic acid catabolic pathway on tomato leaves, apple fruit and bell peppers was unaltered.